Hmmm, you may want to take a look at Terry Pratchett's Jingo, which has a mysterious reappearing island....
Other possibilities-
The Call of Cthulhu Approach - the stars are now right, and the great temple has arisen. Now the ceremonies and sacrifices must begin on the great tower/pyramid to awaken a sleeping god! Guess who arrives in the nick of time to throw a spanner into the works?
The Lost Dutchman Approach - Long ago a wicked man made a deal with the dark powers, committing a great sin in return for eternal life. Now he despairs of that life ever ending, bound to his tower, and loosed in the waking world only once in a hundred years, oh, how he longs for death... perhaps the heroes' swords will be the ones that release him.
The Repentant Approach - much the same as above, but he is truly repenting of his sins, and seeks to perform a final good act that will release him from his chains.
The Trap Approach - the island only appears every hundred years, but when it sinks all those who were there when she went down remain bound in undeath... where do you think all the undead nasties came from, anyway? And the sigils on the walls lie about when it sinks....
The Great Tide Approach - the tower does not rise, it is in a narrow bay that is completely drained once in a hundred years, when the moon and sun are aligned just so..... and when the tide returns it does so in a manner that makes the
Bay of Fundy seem tame.
The Draw Down Approach - much like above, only it is in the lake formed by a great dwarfen dam. Once a century the dwarfs drain the water so they can tend to the dam. Not only a tower but an entire town was submerged, whether the people made it out depends on how nice your dwarfs are....
The Ghost Approach - the whole place is nothing but a ghost, or a ghost's memories. When the time comes right the tower does not sink, but disappears with the fog. It sank all those years ago, but memories and dreams can hold strange weight. Lay the spirit to rest and the tower fades, never to return.
For many of them I would leave the lower reaches flooded, with the level at the water line about waist deep, and slimy as all heck.
The Auld Grump